Many important cellular processes are regulated by reaction-diffusion (RD) of molecules that takes place both in the cytoplasm and on the membrane. To model and analyze such multicompartmental...
A web server for interactive and zoomable Chaos Game Representation images (2009)
Arakawa, Kazuharu, Oshita, Kazuki, Tomita, Masaru
Abstract Chaos Game Representation (CGR) is a generalized scale-independent Markov transition table, which is useful for the visualization and comparative study of genomic signature, or for the study...
The-Cell System is an advanced open-source simulation platform to model and analyze biochemical reaction networks. The present algorithm modules of the system assume that the reacting molecules are...
Measure of synonymous codon usage diversity among genes in bacteria (2009)
Suzuki, Haruo, Saito, Rintaro, Tomita, Masaru
Abstract Background In many bacteria, intragenomic diversity in synonymous codon usage among genes has been reported. However, no quantitative attempt has been made to compare the diversity levels...
長期保存赤血球代謝のシミュレーションによる予測とメタボローム解析による実証 (2009)
西野, 泰子, ニシノ, タイコ, Nishino, Taiko, 冨田, 勝, トミタ, マサル, Tomita, Masaru
Author
谷内江, 望, ヤチエ, ノゾム, Yachie, Nozomu, 冨田, 勝, トミタ, マサル, Tomita, Masaru, ...
Author
Computational analysis of RNA splicing mediated post-transcriptional regulation (2009)
菅原, 潤一, スガハラ, ジュンイチ, Sugahara, Junichi, 冨田, 勝, トミタ, マサル, Tomita, Masaru, ...
Author
A Software Engineering Approach (2009)
cellular processes involves diverse components and complex interactions. To successfully model such processes, simulation systems must meet a number of computational requirements, including an...
Genome Projector: zoomable genome map with multiple views (2009)
Arakawa, Kazuharu, Tamaki, Satoshi, Kono, Nobuaki, Kido, Nobuhiro, Ikegami, Keita, Ogawa, Ryu, ...
Abstract Background Molecular biology data exist on diverse scales, from the level of molecules to -omics. At the same time, the data at each scale can be categorised into multiple layers, such as...
Kanai, Akio, Sato, Asako, Fukuda, Yoko, Okada, Kiyoshi, Matsuda, Takashi, Sakamoto, Taiichi, ...
Using an expression protein library of a hyperthermophilic archaeon, Pyrococcus furiosus, we identified a gene (PF0027) that encodes a protein with heat-stable cyclic nucleotide phosphodiesterase...
GeNESiS: gene network evolution simulation software (2008)
Kratz, Anton, Tomita, Masaru, Krishnan, Arun
Abstract Background There has been a lot of interest in recent years focusing on the modeling and simulation of Gene Regulatory Networks (GRNs). However, the evolutionary mechanisms that give rise to...
Time-resolved metabolomics reveals metabolic modulation in rice foliage (2008)
Sato, Shigeru, Arita, Masanori, Soga, Tomoyoshi, Nishioka, Takaaki, Tomita, Masaru
Abstract Background To elucidate the interaction of dynamics among modules that constitute biological systems, comprehensive datasets obtained from "omics" technologies have been used. In recent...
Prediction of Protein Subcellular Localization Using an Artificial Neural Network (2008)
Anton Kratz, Rintaro Saito, Arun Krishnan, Masaru Tomita
Experimental methods for determining protein localization can not keep up with the speed at which genomic sequences are being generated. There has been extensive research in computational methods for...
Masaru Tomita, Marion Kee, Hiroaki Saito, Teruko Mitamura, Hideto Tomabechi
We describe our Universal Parser Architecture and its use in a speech translation system, based on the Machine Translation system under development at the Center for Machine Translation at Carnegie...
312 Genome Informatics 12: 312–313 (2001) Towards Simulation of Whole Metabolic Pathways in (2008)
Human Erythrocyte, Ayako Kinoshita, Yoichi Nakayama, Masaru Tomita
We have previously reported the simulation of the glucose-6-phosphate dehydrogenase (G6PD) deficiency in human erythrocyte using E-CELL system. In this previous work, we showed that the glutathione...
Development of E-Cell kinetic model interoperability environment (2008)
Tatsuya Ishida, Takeshi Sakurada, Tomoya Kitayama, Masaru Tomita
Keywords: systems biology, model repository, cell simulation, the E-Cell system
Distributed Cell Biology Simulations with E-Cell System (2008)
Masahiro Sugimoto, Kouichi Takahashi, Tomoya Kitayama, Daiki Ito, Masaru Tomita
Abstract. Many useful applications of simulation in computational cell biology, e.g. kinetic parameter estimation, Metabolic Control Analysis (MCA), and bifurcation analysis, require a large number...
BIOINFORMATICS ORIGINAL PAPER (2008)
Genome Analysis, Noriyuki Kitagawa, Takanori Washio, Shunichi Kosugi, Tomoya Yamashita, Kenji Higashi, ...
Vol. 21 no. 9 2005, pages 1758–1763 doi:10.1093/bioinformatics/bti253 Computational analysis suggests that alternative first exons are involved in tissue-specific transcription in rice (Oryza...
Sachi Inagaki, Koji Numata, Takefumi Kondo, Masaru Tomita, Kunio Yasuda, Akio Kanai, ...
One of the most surprising results to emerge from mammalian cDNA sequencing projects is that thousands of mRNA-like non-coding RNAs (ncRNAs) are expressed and constitute at least 10% of poly(A) +...
Statistical Characterization of Transcription Start Sites (2008)
In Plant Genomes, Shigeo Fujimori, Takanori Washio, Masaru Tomita
Although large amounts of genomic and full-length cDNA sequence data from plants are now publicly available, knowledge of the promoters and transcription start sites (TSSs) in plants is still limited...
Electrophysiological simulation of developmental changes in cardiomyocytes (2008)
伊藤, ひとみ, イトウ, ヒトミ, Ito, Hitomi, 冨田, 勝, トミタ, マサル, Tomita, Masaru, ...
Author
細菌の増殖抑制効果を有する人工低分子RNAの大規模解析 (2008)
小正, 瑞季, コマサ, ミズキ, Komasa, Mizuki, 冨田, 勝, トミタ, マサル, Tomita, Masaru, ...
Author
Laborde, Thomas, Tomita, Masaru, Krishnan, Arun
Abstract Background It has long been known that small regions of proteins tend to fold independently and are then stabilized by interactions between these distinct subunits or modules. Such units,...
Kazuharu Arakawa, Reina Uno, Yoichi Nakayama, Masaru Tomita
A Chi sequence (5’-GCTGGTGG-3’) in Escherichia coli is an 8bp sequence element that promotes recombination by attenuating the activity of RecBCD enzyme. Upon recognition of the Chi sequence, the...
Appficafio ~ of the Direct Memory Access paradigm to (2008)
I~deto Comabechi, Masaru Tomita
~,ot ~ °~a ~ ~a~gl~age interfaces to knowledge-based systems
Analysis of gene expression for novel anti-tDNA transcripts in Escherichia coli (2008)
新原, 温子, シンハラ, アツコ, Shinhara, Atsuko, 松井, 求, マツイ, モトム, Matsui, Motomu, ...
Author
Kyota Ishii Tamayo, Tamayo Uechi, Takanori Washio, Maki Yoshihama, Naoya Kenmochi, Masaru Tomita
Introduction The human 80S ribosome was composed with 79 ribosomal proteins (RPs) and 4 rRNAs. Although all of RP genes have been thought to have an identical transcriptional and translational...
Genome Informatics 14: 294--295 (2003) E - Cell System Version 3: A Software Platform for (2008)
Integrative Computational Biology, Kouichi Takahashi, Takeshi Sakurada, Kazunari Kaizu, Tomoya Kitayama, Satya Arjunan, ...
Introduction E - Cell System is an OpenSource software environment for modeling, simulation and mathematical analysis of the cell (http://www.e-cell.org/software). Unlike its preceding versions, E -...
Thomas Laborde, Masaru Tomita, Arun Krishnan
Software GANDivAWeb: A web server for detecting early folding units ("foldons") from protein 3D structures
Shinoda, Kosaku, Tomita, Masaru, Ishihama, Yasushi
Motivation: Liquid chromatography-tandem mass spectrometry (LC-MS/MS) is a powerful tool in proteomics studies, but when peptide retention information is used for identification purposes, it remains...
Reshuffling of the Bacillus subtilis 168 Genome by Multifold Inversion (2008)
Kuroki, Azusa, Toda, Tsutomu, Matsui, Kuniko, Uotsu-Tomita, Rie, Tomita, Masaru, Itaya, Mitsuhiro
The genome of Bacillus subtilis 168 was modified to yield a genome vector for the cloning of DNA several Mb in size. Unlike contemporary plasmid-based vectors, this 4.2 Mb genome vector requires...
Comparative expression analysis uncovers novel features of endogenous antisense transcription (2008)
Okada, Yuki, Tashiro, Chiaki, Numata, Koji, Watanabe, Kazufumi, Nakaoka, Hajime, Yamamoto, Naoyuki, ...
Increasing numbers of sense–antisense transcripts (SATs), which are transcribed from the same chromosomal location but in opposite directions, have been identified in various eukaryotic species,...
Sugahara, Junichi, Kikuta, Kaoru, Fujishima, Kosuke, Yachie, Nozomu, Tomita, Masaru, Kanai, Akio
The analysis of archaeal tRNA genes is becoming more important to evaluate the origin and evolution of tRNA molecule. Even with the recent accumulation of complete genomes of numerous archaeal...
CMU MT ToolKit version 8-5 (2007)
This paper describes a software package that consists of the following three major components:
Sergei Nirenburg, Jaime Carbonell, Masaru Tomita, Kenneth Goodman, Kenneth Goodman, Sergei Nirenburg (editors, ...
Machine translation (MT) research in the United States has enjoyed a bit of a revival in the last several years. Building on research in semantic analysis from both natural language processing and...
Yoichi Nakayama, Ayako Kinoshita, Masaru Tomita
We previously reported a computer model of the human erythrocyte using E-CELL simulation system [1, 2]. The model has three major metabolic pathways, including glycolysis, the pentose phosphate...
Correlation between Sequence Conservation of 5 ’ UTR and Codon Usage Bias (2007)
Hiroaki Sakai, Yusuke Ohkuma, Chiaki Imamura, Akira Shinagawa, Masayoshi Itoh, Kazuhiro Shibata, ...
Keywords: codon usage bias, Kozak’s consensus sequence, translation efficiency
Computer Simulation of Glycolysis in Pancreatic β-Cells Using the E-CELL System (2007)
All vertebrates use insulin-producing pancreatic β-cells to keep track of the levels of the predominant small nutrient molecules in blood by accurately measuring the concentrations of glucose, amino...
We have been constructing a kinetic model of mitochondrial energy metabolism using the E-Cell system [2, 3], a generic simulation environment we have developed for whole cell simulation. The model...
Emily Wang, Yoichi Nakayama, Masaru Tomita
The E-CELL system is a generic software package for whole cell modeling and simulation developed by the Laboratory for Bioinformatics at Keio University [1]. Photosynthesis is generally characterized...
Modeling of Transcription and DNA Replication Using the E-CELL Simulation System (2007)
Kenta Hashimoto, Fumihiko Miyoshi, Thomas S. Shimizu, Takeshi Satoyoshi, Masaru Tomita
2 Graduate School of Media and Governance 3 DepartmentofEnvironmental Information
Comprehensive Sequence Analyses of 5 ' Flanking Regions of Primate Alu Elements (2007)
Yoshimi Toda, Rintaro Saito, Masaru Tomita
Retrotransposons have been generally known to integrate randomly into host genomes. Jurka (1997) [3], however, showed consensus sequence patterns at integration sites of certain mammalian...
Modeling of Transcription and DNA Replication Using the E-CELL Simulation System (2007)
Kenta Hashimoto, Fumihiko Miyoshi, Thomas S. Shimizu, Takeshi Satoyoshi, Masaru Tomita
1 Laboratory for Bioinformatics 2 Graduate School of Media and Governance 3
Taku Okada, Masaru Tomita, Kazuhiko Kawasaki, Shinsei Minoshima
Nobuyoshi Shimizu 4
Yuko Osada, Rintaro Saito, Masaru Tomita
3 DepartmentofEnvironmental Information
Although the Shine-Dalgarno (SD) sequence [5] is widely accepted as the signal sequence for ribosomemRNA binding in procaryotic translation initiation, this sequence is not well conserved among genes...
Yoshimi Toda, Rintaro Saito, Masaru Tomita
Retrotransposons have been generally known to integrate randomly into host genomes. Jurka (1997) [3], however, showed consensus sequence patterns at integration sites of certain mammalian...
Yuko Osada, Rintaro Saito, Masaru Tomita
2 Graduate School of Media and Governance 3
On Periodicity of Adenine-Adenine Dinucleotides in Bacterial Genomes (2007)
Masahiko Wada, Yukihiro Kawashima, Masaru Tomita
3
On Periodicity of Adenine-Adenine Dinucleotides in Bacterial Genomes (2007)
Masahiko Wada, Yukihiro Kawashima, Masaru Tomita
DepartmentofEnvironmental Information
In Silico Simulation Represents Adenoviral Gene Knockdown of Myocardial Ventricular Cell (2007)
Yasuhiro Naito, Motohiro Yoneda, Sayaka Ishinabe, Shoko Miyamoto, Akinori Noma, ...
Keywords: E-Cell, Kyoto model, cell simulation, ion channel
Development of Bacteria Analysis System v.2 on the G-Language Genome Analysis Environment (2007)
Daisuke Kyuma, Kazuharu Arakawa, Koya Mori, Masaru Tomita
Keywords: G-language Genome Analysis Environment, analysis software, computational analysis
Prediction of Biochemical Reactions Using Genetic Programming (2007)
Masahiro Sugimoto, Shinichi Kikuchi, Masaru Tomita
estimation, mathematical model
Automatic Generation of Cell-Wide Pathway Model from Complete Genome (2007)
Kazuharu Arakawa, Yohei Yamada, Hiromi Komai, Kosaku Shinoda, Yoichi Nakayama, Masaru Tomita
Knowledge in molecular biology is rapidly accumulating in the fields of genome, transcriptome, proteome, and metabolome, demanding for a systems biology approach in order to view the dynamic behavior...
Haruo Suzuki, Rintaro Saito, Masaru Tomita
balance
Toward large-scale modeling of Escherichia coli (2007)
石井, 伸佳, イシイ, ノブヨシ, Ishii, Nobuyoshi, 冨田, 勝, トミタ, マサル, Tomita, Masaru
Author
Analysis of stop codon readthrough utilizing comparative genomics approach (2007)
服部, 美樹子, ハットリ, ミキコ, Hattori, Mikiko, 冨田, 勝, トミタ, マサル, Tomita, Masaru, ...
Author
Morohashi, Mineo, Ohashi, Yoshiaki, Tani, Saeka, Ishii, Kotaro, Itaya, Mitsuhiro, Nanamiya, Hideaki, ...
The soil bacterium Bacillus subtilis forms dormant, robust spores as a tactic to ensure survival under conditions of starvation. However, the sporulating culture includes sporulating and...
ヒト赤血球代謝シミュレーションモデルを用いた低温保存血液における赤血球代謝動態の予測と解析 (2007)
西野, 泰子, ニシノ, ヤスコ, Nishino, Yasuko, 冨田, 勝, トミタ, マサル, Tomita, Masaru
Author
Evolution of ribonuclease H genes in prokaryotes to avoid inheritance of redundant genes (2007)
Kochiwa, Hiromi, Tomita, Masaru, Kanai, Akio
Abstract Background A theoretical model of genetic redundancy has proposed that the fates of redundant genes depend on the degree of functional redundancy, and that functionally redundant genes will...
Fujishima, Kosuke, Komasa, Mizuki, Kitamura, Sayaka, Suzuki, Haruo, Tomita, Masaru, Kanai, Akio
Proteins play a critical role in complex biological systems, yet about half of the proteins in publicly available databases are annotated as functionally unknown. Proteome-wide functional...
Consideration on Contact Mechanism of YBaCuO Bulk Superconductor with Deposited Metal Layer (2007)
FUJITA, Hiroyuki, FUKUDA, Katsuya, SAWA, Koichiro, TOMITA, Masaru, MURAKAMI, Masato, SAKAI, Naomichi, ...
A persistent current switch (PCS) is used for superconducting applications, such as superconducting magnetic energy storage (SMES) system. The authors have proposed a mechanical switch of Y-Ba-Cu-O...
Distinguishing enzymes using metabolome data for the hybrid dynamic/static method (2007)
Ishii, Nobuyoshi, Nakayama, Yoichi, Tomita, Masaru
Abstract Background In the process of constructing a dynamic model of a metabolic pathway, a large number of parameters such as kinetic constants and initial metabolite concentrations are required....
Sugahara, Junichi, Yachie, Nozomu, Arakawa, Kazuharu, Tomita, Masaru
In archaeal species, several transfer RNA genes have been reported to contain endogenous introns. Although most of the introns are located at anticodon loop regions between nucleotide positions 37...
ゲノムの変化と秩序 : レトロトランスポゾンの転位の痕跡からヌクレオソームポジショニングを浮き彫りにする (2007)
芦田, 広樹, アシダ, ヒロキ, Ashida, Hiroki, 冨田, 勝, トミタ, マサル, Tomita, Masaru
Author
Visualization of three-way comparisons of omics data (2007)
Baran, Richard, Robert, Martin, Suematsu, Makoto, Soga, Tomoyoshi, Tomita, Masaru
Abstract Background Density plot visualizations (also referred to as heat maps or color maps) are widely used in different fields including large-scale omics studies in biological sciences. However,...
藤島, 皓介, フジシマ, コウスケ, Fijishima, Kosuke, 冨田, 勝, トミタ, マサル, Tomita, Masaru
Author
代数学的手法を用いた海馬シグナル伝達機構の解析 (2007)
松原, 嘉哉, マツバラ, ヨシヤ, Matsubara, Yoshiya, 冨田, 勝, トミタ, マサル, Tomita, Masaru
Author
Haruo Suzuki, Rintaro Saito, Masaru Tomita
G + C composition at the third codon position (GC3) is widely reported to be correlated with synonymous codon usage bias. However, no quantitative attempt has been made to compare the extent of this...
Kazuharu Arakawa, Masaru Tomita
Bacterial chromosomes are partly shaped by the functional requirements for efficient replication, which lead to strand bias as commonly characterized by the excess of guanines over cytosines in the...
Kazuharu Arakawa, Masaru Tomita
Circular bacterial chromosomes have highly polarized nucleotide composition in the two replichores, and this genomic strand asymmetry can be visualized using GC skew graphs. Here we propose and...
Kazuharu Arakawa, Masaru Tomita
Circular bacterial chromosomes have highly polarized nucleotide composition in the two replichores, and this genomic strand asymmetry can be visualized using GC skew graphs. Here we propose and...
Haruo Suzuki, Rintaro Saito, Masaru Tomita
G + C composition at the third codon position (GC3) is widely reported to be correlated with synonymous codon usage bias. However, no quantitative attempt has been made to compare the extent of this...
Sugahara, Junichi, Yachie, Nozomu, Arakawa, Kazuharu, Tomita, Masaru
In archaeal species, several transfer RNA genes have been reported to contain endogenous introns. Although most of the introns are located at anticodon loop regions between nucleotide positions 37...
MathDAMP: a package for differential analysis of metabolite profiles (2006)
Baran, Richard, Kochi, Hayataro, Saito, Natsumi, Suematsu, Makoto, Soga, Tomoyoshi, Nishioka, Takaaki, ...
Abstract Background With the advent of metabolomics as a powerful tool for both functional and biomarker discovery, the identification of specific differences between complex metabolite profiles is...
HybGFS: a hybrid method for genome-fingerprint scanning (2006)
Shinoda, Kosaku, Yachie, Nozomu, Masuda, Takeshi, Sugiyama, Naoyuki, Sugimoto, Masahiro, Soga, Tomoyoshi, ...
Abstract Background Protein identification based on mass spectrometry (MS) has previously been performed using peptide mass fingerprinting (PMF) or tandem MS (MS/MS) database searching. However,...
がんメタボローム : 培養細胞および臨床検体を用いた前処理法の確立とメタボローム解析 (2006)
紙, 健次郎, カミ, ケンジロウ, Kami, Kenjiro, 冨田, 勝, トミタ, マサル, Tomita, Masaru
Author
Kitayama, Tomoya, Kinoshita, Ayako, Sugimoto, Masahiro, Nakayama, Yoichi, Tomita, Masaru
Abstract Background In order to improve understanding of metabolic systems there have been attempts to construct S-system models from time courses. Conventionally, non-linear curve-fitting algorithms...
Parameter estimation for stiff equations of biosystems using radial basis function networks (2006)
Matsubara, Yoshiya, Kikuchi, Shinichi, Sugimoto, Masahiro, Tomita, Masaru
Abstract Background The modeling of dynamic systems requires estimating kinetic parameters from experimentally measured time-courses. Conventional global optimization methods used for parameter...
Automatic reconstruction of cell-wide metabolic pathway models from the genome (2006)
荒川, 和晴, アラカワ, カズハル, Arakawa, Kazuharu, 冨田, 勝, トミタ, マサル, Tomita, Masaru
Author
Escherichia coli cell death caused by endonuclease chromosome scission (2006)
東, 憲児, ヒガシ, ケンジ, Higashi, Kenji, 冨田, 勝, トミタ, マサル, Tomita, Masaru
Author
GEM System: automatic prototyping of cell-wide metabolic pathway models from genomes (2006)
Arakawa, Kazuharu, Yamada, Yohei, Shinoda, Kosaku, Nakayama, Yoichi, Tomita, Masaru
Abstract Background Successful realization of a "systems biology" approach to analyzing cells is a grand challenge for our understanding of life. However, current modeling approaches to cell...
Characteristics and clustering of human ribosomal protein genes (2006)
Ishii, Kyota, Washio, Takanori, Uechi, Tamayo, Yoshihama, Maki, Kenmochi, Naoya, Tomita, Masaru
Abstract Background The ribosome is a central player in the translation system, which in mammals consists of four RNA species and 79 ribosomal proteins (RPs). The control mechanisms of gene...
Kosaku Shinoda, Nozomu Yachie, Takeshi Masuda, Naoyuki Sugiyama, Masahiro Sugimoto, Tomoyoshi Soga, ...
This is an Open Access article distributed under the terms of the Creative Commons Attribution License
Gapped Gene Polymerase Chain Assembly : a method for clustering multiple gene fragments (2006)
駒井, 宏美, コマイ, ヒロミ, Komai, Hiromi, 中山, 洋一, ナカヤマ, ヨウイチ, Nakayama, Yoichi, ...
藤沢
TAKAHASHI, HIDEYUKI, HAYASHI, MITSUNORI, GOTO, FUMIYUKI, SATO, SHIGERU, SOGA, TOMOYOSHI, NISHIOKA, TAKAAKI, ...
• Background and Aims Previous studies have shown that transgenic rice plants overexpressing YK1, which possesses dihydroflavonol-4-reductase (DFR) activity, showed biotic and abiotic stress...
Large-scale identification of protein-protein interaction of Escherichia coli K-12 (2006)
Arifuzzaman, Mohammad, Maeda, Maki, Itoh, Aya, Nishikata, Kensaku, Takita, Chiharu, Saito, Rintaro, ...
Protein–protein interactions play key roles in protein function and the structural organization of a cell. A thorough description of these interactions should facilitate elucidation of cellular...
TAKAHASHI, HIDEYUKI, HAYASHI, MITSUNORI, GOTO, FUMIYUKI, SATO, SHIGERU, SOGA, TOMOYOSHI, NISHIOKA, TAKAAKI, ...
• Background and Aims Previous studies have shown that transgenic rice plants overexpressing YK1, which possesses dihydroflavonol-4-reductase (DFR) activity, showed biotic and abiotic stress...
Large-scale identification of protein-protein interaction of Escherichia coli K-12 (2006)
Arifuzzaman, Mohammad, Maeda, Maki, Itoh, Aya, Nishikata, Kensaku, Takita, Chiharu, Saito, Rintaro, ...
Protein–protein interactions play key roles in protein function and the structural organization of a cell. A thorough description of these interactions should facilitate elucidation of cellular...
Yugi, Katsuyuki, Nakayama, Yoichi, Kojima, Shigen, Kitayama, Tomoya, Tomita, Masaru
Abstract Background Elucidating the dynamic behaviour of genetic regulatory networks is one of the most significant challenges in systems biology. However, conventional quantitative predictions have...
Hybrid dynamic/static method for large-scale simulation of metabolism (2005)
Yugi, Katsuyuki, Nakayama, Yoichi, Kinoshita, Ayako, Tomita, Masaru
Abstract Background Many computer studies have employed either dynamic simulation or metabolic flux analysis (MFA) to predict the behaviour of biochemical pathways. Dynamic simulation determines the...
多種生物ゲノムのコンピューター解析によるSplit-tRNA遺伝子の予測 (2005)
菅原, 潤一, スガハラ, ジュンイチ, Sugahara, Junichi, 冨田, 勝, トミタ, マサル, Tomita, Masaru
Author
Nakayama, Yoichi, Kinoshita, Ayako, Tomita, Masaru
Abstract Background Cell simulation, which aims to predict the complex and dynamic behavior of living cells, is becoming a valuable tool. In silico models of human red blood cell (RBC) metabolism...
GC-compositional strand bias around transcription start sites in plants and fungi (2005)
Fujimori, Shigeo, Washio, Takanori, Tomita, Masaru
Abstract Background A GC-compositional strand bias or GC-skew (=(C-G)/(C+G)), where C and G denote the numbers of cytosine and guanine residues, was recently reported near the transcription start...
BMC Bioinformatics BioMed Central (2005)
Katsuyuki Yugi, Yoichi Nakayama, Shigen Kojima, Tomoya Kitayama, Masaru Tomita
Research article A microarray data-based semi-kinetic method for predicting quantitative dynamics of genetic networks
Kouichi Takahashi, Satya N, A Vel Arjunan, Masaru Tomita
Abstract How cells utilize intracellular spatial features to optimize their signaling characteristics is still not clearly understood. The physical distance between the cell-surface receptor and the...
BMC Bioinformatics BioMed Central (2005)
Research article Parameter estimation for stiff equations of biosystems using radial basis function networks
Kitagawa, Noriyuki, Washio, Takanori, Kosugi, Shunichi, Yamashita, Tomoya, Higashi, Kenji, Yanagawa, Hiroshi, ...
Motivation: Transcription start site selection and alternative splicing greatly contribute to diversifying gene expression. Recent studies have revealed the existence of alternative first exons, but...
Kitagawa, Noriyuki, Washio, Takanori, Kosugi, Shunichi, Yamashita, Tomoya, Higashi, Kenji, Yanagawa, Hiroshi, ...
Motivation: Transcription start site selection and alternative splicing greatly contribute to diversifying gene expression. Recent studies have revealed the existence of alternative first exons, but...
線虫(C. elegans)をもちいたmicroRNA標的認識配列の解析 (2004)
渡邊, 由香, ワタナベ, ユカ, Watanabe, Yuka, 冨田, 勝, トミタ, マサル, Tomita, Masaru
Author
高橋, 恒一, タカハシ, コウイチ, Takahashi, Kouichi, 冨田, 勝, トミタ, マサル, Tomita, Masaru
Author
Computational and molecular biological analysis of overlapping genes in bacterial genomes (2004)
福田, 陽子, フクダ, ヨウコ, Fukuda, Yoko, 冨田, 勝, トミタ, マサル, Tomita, Masaru
Author
A Multi-Algorithm, Multi-Timescale Method for Cell Simulation (2004)
Kouichi Takahashi, Kazunari Kaizu, Bin Hu, Masaru Tomita
Motivation Many important problems in cell biology require the dense nonlinear interactions between functional modules to be considered. The importance of computer simulation in understanding...
E-CELL Systemを用いたバクテリアの環境応答のシミュレーション (2004)
松崎, 由理, マツザキ, ユリ, Matsuzaki, Yuri, 冨田, 勝, トミタ, マサル, Tomita, Masaru
藤沢
A multi-algorithm, multi-timescale method for cell simulation (2004)
Takahashi, Kouichi, Kaizu, Kazunari, Hu, Bin, Tomita, Masaru
Motivation Many important problems in cell biology require the dense nonlinear interactions between functional modules to be considered. The importance of computer simulation in understanding...
A general computational model of mitochondrial metabolism in a whole organelle scale (2004)
Yugi, Katsuyuki, Tomita, Masaru
Summary: A computational tool for mitochondrial systems biology has been developed as a simulation model of ECell2, a publicly available simulation system. The general model consists of 58 enzymatic...
A multi-algorithm, multi-timescale method for cell simulation (2004)
Takahashi, Kouichi, Kaizu, Kazunari, Hu, Bin, Tomita, Masaru
Motivation: Many important problems in cell biology require the dense nonlinear interactions between functional modules to be considered. The importance of computer simulation in understanding...
ITOH, HITOMI, WASHIO, TAKANORI, TOMITA, MASARU
We previously reported a computational approach to infer alternative splicing patterns from Mus musculus full-length cDNA clones and microarray data. Although we predicted a large number of...
A general computational model of mitochondrial metabolism in a whole organelle scale (2004)
Yugi, Katsuyuki, Tomita, Masaru
Summary: A computational tool for mitochondrial systems biology has been developed as a simulation model of E-Cell2, a publicly available simulation system. The general model consists of 58 enzymatic...
Ohtani, Naoto, Yanagawa, Hiroshi, Tomita, Masaru, Itaya, Mitsuhiro
ST0753, the orthologous gene of Type 1 RNase H found in a thermoacidophilic archaeon, Sulfolobus tokodaii, was analyzed. The recombinant ST0753 protein exhibited RNase H activity in both in vivo and...
A multi-algorithm, multi-timescale method for cell simulation (2004)
Takahashi, Kouichi, Kaizu, Kazunari, Hu, Bin, Tomita, Masaru
Motivation Many important problems in cell biology require the dense nonlinear interactions between functional modules to be considered. The importance of computer simulation in understanding...
A general computational model of mitochondrial metabolism in a whole organelle scale (2004)
Yugi, Katsuyuki, Tomita, Masaru
Summary: A computational tool for mitochondrial systems biology has been developed as a simulation model of ECell2, a publicly available simulation system. The general model consists of 58 enzymatic...
完全長cDNAおよび5'端読み配列を用いた選択的プロモーターの解析 (2003)
北川, 統之, キタガワ, ノリユキ, Kitagawa, Noriyuki, 冨田, 勝, トミタ, マサル, Tomita, Masaru
Author
Kosuke Fujishima, Jun Imoto, Akio Kanai, Masaru Tomita
Keywords: proteome, amino acid frequency, amino acid periodicity, archaea, RNA-binding protein
Translational Efficiency Prediction Using Structural Learning Method (2003)
Koya Mori, Rintaro Saito, Shinichi Kikuchi, Masaru Tomita
It has been shown that sequence patterns including Shine-Dalgarno sequences, start codons and those in between have effect on translational efficiencies. However relationships between these patterns...
Model Construction of the Energy Metabolism Pathway in Myocardial Cell (2003)
In Myocardial Cell, Motohiro Yoneda, Shoko Miyamoto, Yasuhiro Naito, Sayaka Ishinabe, Satoshi Matsuoka, ...
Introduction Myocardial cell has simple outputs, such as membrane potential and muscle contraction, which integrate many elementary processes, and a vast quantity of data is available from the patch...
Integrated Distributed Computing Environment on the G-Language GAE v.2 (2003)
Ryo Hattori, Kazuharu Arakawa, Hayataro Kouchi, Masaru Tomita
this paper, we report the development and implementation of the distributed computing environment utilizing database management system and client-server architecture.In order to analyze the huge...
Identifying Potential Regulatory Sequences of Alternative Splicing (2003)
Hitomi Itoh, Takanori Washio, Masaru Tomita
Introduction Alternative splicing is an important mechanism that contributes to expanding protein diversity by generating multiple protein isoforms from a single gene. We have previously reported...
Microarray Visualization System on the G-Language GAE (2003)
Yohei Yamada, Kazuharu Arakawa, Hirotada Mori, Masaru Tomita
Introduction In this work, we have developed the Microarray Visualization System over the generic bioinformatics workbench G-language Genome Analysis Environment (G-language GAE) [5] which...
G-Language Genome Analysis Environment Version 2 (2003)
Hayataro Kouchi, Kazuharu Arakawa, Ryo Hattori, Yohei Yamada, Yusuke Kobayashi, Atsuko Kishi, ...
Introduction G-language Project of Institute for Advanced Biosciences aims to introduce higher e#ciency in genome analysis by: 1. Constructing an integrated environment for the development of...
Nozomu Yachie, Koji Numata, Rintaro Saito, Akio Kanai, Masaru Tomita
Introduction Non-coding RNAs (ncRNAs) are thought to act as structural, regulatory or catalytic molecules, while messenger RNAs (mRNAs) are intermediated RNA molecules, which are translated to...
Identification of Putative Noncoding RNAs Among the RIKEN Mouse Full-Length cDNA Collection (2003)
Numata, Koji, Kanai, Akio, Saito, Rintaro, Kondo, Shinji, Adachi, Jun, Wilming, Laurens G., ...
With the sequencing and annotation of genomes and transcriptomes of several eukaryotes, the importance of noncoding RNA (ncRNA)—RNA molecules that are not translated to protein products—has...
Dynamic modeling of genetic networks using genetic algorithm and S-system (2003)
Kikuchi, Shinichi, Tominaga, Daisuke, Arita, Masanori, Takahashi, Katsutoshi, Tomita, Masaru
Motivation: The modeling of system dynamics of genetic networks, metabolic networks or signal transduction cascades from time-course data is formulated as a reverse-problem. Previous studies focused...
Computational analysis of stop codon readthrough in D.melanogaster (2003)
Sato, Misaki, Umeki, Hitomi, Saito, Rintaro, Kanai, Akio, Tomita, Masaru
Motivation: Readthrough is an unusual process in which a stop codon is misread or skipped. Recently it has been shown that some translation is regulated by the readthrough reactions although the...
選択的スプライシングにおけるラリアット分岐配列の解析 (2002)
伊藤, ひとみ, イトウ, ヒトミ, Ito, Hitomi, 冨田, 勝, トミタ, マサル, Tomita, Masaru
Author
G-language project : 汎用ゲノム解析ソフトウェアの開発 (2001)
森, 航哉, モリ, コウヤ, Mori, Koya, 冨田, 勝, トミタ, マサル, Tomita, Masaru
Author
バクテリアゲノムにおける組換え促進配列χ配列の解析 (2001)
鵜野, レイナ, ウノ, レイナ, Uno, Reina, 冨田, 勝, トミタ, マサル, Tomita, Masaru
Author
E-CELL Systemを用いた出芽酵母の細胞周期シミュレーション (2001)
藤田, 由起, フジタ, ユキ, Fujita, Yuki, 冨田, 勝, トミタ, マサル, Tomita, Masaru
Author
同義語コドン使用の偏りと5'非翻訳領域の保存性の関係のコンピュータ解析 (2001)
坂井, 寛章, サカイ, ヒロアキ, Sakai, Hiroaki, 冨田, 勝, トミタ, マサル, Tomita, Masaru
Author
E-CELL simulation environmentにおけるパラメータ推定機構の開発 (2000)
齋藤, 裕介, サイトウ, ユウスケ, Saito, Yusuke, 冨田, 勝, トミタ, マサル, Tomita, Masaru
Author
小知和, 裕美, コチワ, ヒロミ, Kochiwa, Hiromi, 冨田, 勝, トミタ, マサル, Tomita, Masaru
Author
ストップコドン周辺に出現する顕著なパターンの解析 (1999)
小澤, 陽介, オザワ, ヨウスケ, Ozawa, Yosuke, 冨田, 勝, トミタ, マサル, Tomita, Masaru
Author
バクテリアゲノムにおける複製開始地点のコンピュータ解析 (1998)
坂井, 寛章, サカイ, ヒロアキ, Sakai, Hiroaki, 冨田, 勝, トミタ, マサル, Tomita, Masaru
Author
E-CELL project overview: towards integrative simulation of cellular processes (1998)
Masaru Tomita, Kenta Hashimoto, Kouichi Takahashi, Yuri Matsuzaki, Ryo Matsushima, Kanako Saito, ...
12 Hisako Nakano 14
Yuri Matsuzaki, Kanako Saito, Tom Shimizu, Masaru Tomita
2 Graduate School of Media and Governance 3 DepartmentofEnvironmental Information
Yusuke Saito, Kouichi Takahashi, Masaru Tomita
We applied multivariate time series analysis to metabolic models constructed using the E-CELL system. The E-CELL system [1] is a generic simulation environment for modeling cellular processes at...
Yoko Fukuda, Takanori Washio, Masaru Tomita
pneumoniae
Yoko Fukuda, Takanori Washio, Masaru Tomita
DepartmentofEnvironmental Information 3
E-CELL project overview: towards integrative simulation of cellular processes (1998)
Masaru Tomita, Kenta Hashimoto, Kouichi Takahashi, Yuri Matsuzaki, Ryo Matsushima, Kanako Saito, ...
12 Hisako Nakano 14
Yuri Matsuzaki, Kanako Saito, Tom Shimizu, Masaru Tomita
2 Graduate School of Media and Governance 3
Efficient Generalized LR Parsing of Word Lattices (1993)
A word lattice is an efficient representation of a large set of possible sentence candidates, of which only a few are grammaticaland thus parsable. Word lattices are a common output of some speech...
GLR* -- An Efficient Noise-skipping Parsing Algorithm For Context Free Grammars (1993)
Alon Lavie And, Alon Lavie, Masaru Tomita
This chapter describes GLR*, a parser that can parse any input sentence by ignoring unrecognizable parts of the sentence. Using an efficient algorithm, the parser is capable of finding and parsing a...
GLR* - An Efficient Noise-skipping Parsing Algorithm For Context Free Grammars (1993)
This paper describes GLR*, a parser that can parse any input sentence by ignoring unrecognizable parts of the sentence. In case the standard parsing procedure fails to parse an input sentence, the...
GLR* - An Efficient Noise-skipping Parsing Algorithm For Context Free Grammars (1993)
This chapter describes GLR*, a parser that can parse any input sentence by ignoring unrecognizable parts of the sentence. Using an efficient algorithm, the parser is capable of finding and parsing a...
Japanese Technology Evaluation Center (1992)
Jaime Carbonell Chair, David Johnson, Masaru Tomita, Muriel Vasconcellos, Yorick Wilks
Coordinated by Z9/82 0049782
Current issues in parsing technology / edited by Masaru Tomita (1991)
Incluye bibliografía e índice
The Generalized LR Parser/Compiler V8-4: A Software Package for Practical NL Projects (1990)
This paperldescribes a software package designed for practical projects which involve natural language parsing.]he Generalized LR Parser/Compiler V8-4 is based on Tomita's Generalized LR Parsing...
Natural-language understanding (1987)
Philip J. Hayes, Er G. Hauptmann, Jaime G. Carbonell, Masaru Tomita
Parsing spoken input introduces serious problems not present in parsing typed natural language. In particular, indeterminacies and inaccuracies of acoustic recognition must be handled in an integral...
An efficient augmented-context-free parsing algorithm (1987)
An efficient parsing algorithm for augmented context-free grammars is introduced, and its application to on-line natural language interfaces discussed. The algorithm is a generalized LR parsing...
Thesis (Ph. D.)--Carnegie-Mellon University, 1985.
An efficient context-free parsing algorithm for natural languages and its applications / (1985)
"May 1985."
Efficient parsing for natural language : a fast algorithm for practical systems (1985)
Bibliography: p. 193-198
Inferring Alternative Splicing Patterns in Mouse from a Full-Length cDNA Library and Microarray Data
Kochiwa, Hiromi, Suzuki, Ryosuke, Washio, Takanori, Saito, Rintaro, Bono, Hidemasa, ...
Although many studies on alternative splicing of specific genes have been reported in the literature, the general mechanism that regulates alternative splicing has not been clearly understood. In...
Identification of Putative Noncoding RNAs Among the RIKEN Mouse Full-Length cDNA Collection
Numata, Koji, Kanai, Akio, Saito, Rintaro, Kondo, Shinji, Adachi, Jun, Wilming, Laurens G., ...
With the sequencing and annotation of genomes and transcriptomes of several eukaryotes, the importance of noncoding RNA (ncRNA)—RNA molecules that are not translated to protein products—has...
Comparative Analysis of Physical Maps of Four Bacillus subtilis (natto) Genomes
Qiu, Dongru, Fujita, Kyoko, Sakuma, Yuko, Tanaka, Teruo, Ohashi, Yoshiaki, Ohshima, Hideyuki, ...
The complete SfiI and I-CeuI physical maps of four Bacillus subtilis (natto) strains, which were previously isolated as natto (fermented soybean) starters, were constructed to elucidate the genome...
Cleavage of double-stranded RNA by RNase HI from a thermoacidophilic archaeon, Sulfolobus tokodaii 7
Ohtani, Naoto, Yanagawa, Hiroshi, Tomita, Masaru, Itaya, Mitsuhiro
ST0753, the orthologous gene of Type 1 RNase H found in a thermoacidophilic archaeon, Sulfolobus tokodaii, was analyzed. The recombinant ST0753 protein exhibited RNase H activity in both in vivo and...
Ohtani, Naoto, Yanagawa, Hiroshi, Tomita, Masaru, Itaya, Mitsuhiro
All the archaeal genomes sequenced to date contain a single Type 2 RNase H gene. We found that the genome of a halophilic archaeon, Halobacterium sp. NRC-1, contains an open reading frame with...
Hybrid dynamic/static method for large-scale simulation of metabolism
Yugi, Katsuyuki, Nakayama, Yoichi, Kinoshita, Ayako, Tomita, Masaru
A microarray data-based semi-kinetic method for predicting quantitative dynamics of genetic networks
Yugi, Katsuyuki, Nakayama, Yoichi, Kojima, Shigen, Kitayama, Tomoya, Tomita, Masaru
ITOH, HITOMI, WASHIO, TAKANORI, TOMITA, MASARU
We previously reported a computational approach to infer alternative splicing patterns from Mus musculus full-length cDNA clones and microarray data. Although we predicted a large number of...
GEM System: automatic prototyping of cell-wide metabolic pathway models from genomes
Arakawa, Kazuharu, Yamada, Yohei, Shinoda, Kosaku, Nakayama, Yoichi, Tomita, Masaru
Characteristics and clustering of human ribosomal protein genes
Ishii, Kyota, Washio, Takanori, Uechi, Tamayo, Yoshihama, Maki, Kenmochi, Naoya, Tomita, Masaru
Archaeal Pyrococcus furiosus thymidylate synthase 1 is an RNA-binding protein
Kanai, Akio, Sato, Asako, Imoto, Jun, Tomita, Masaru
Using a stem–loop RNA oligonucleotide (19-mer) containing an AUG sequence in the loop region as a probe, we screened the protein library from a hyperthermophilic archaeon, Pyrococcus furiosus, and...
Parameter estimation for stiff equations of biosystems using radial basis function networks
Matsubara, Yoshiya, Kikuchi, Shinichi, Sugimoto, Masahiro, Tomita, Masaru
Large-scale identification of protein–protein interaction of Escherichia coli K-12
Arifuzzaman, Mohammad, Maeda, Maki, Itoh, Aya, Nishikata, Kensaku, Takita, Chiharu, Saito, Rintaro, ...
Protein–protein interactions play key roles in protein function and the structural organization of a cell. A thorough description of these interactions should facilitate elucidation of cellular...
HybGFS: a hybrid method for genome-fingerprint scanning
Shinoda, Kosaku, Yachie, Nozomu, Masuda, Takeshi, Sugiyama, Naoyuki, Sugimoto, Masahiro, Soga, Tomoyoshi, ...
Inferring Alternative Splicing Patterns in Mouse from a Full-Length cDNA Library and Microarray Data
Kochiwa, Hiromi, Suzuki, Ryosuke, Washio, Takanori, Saito, Rintaro, Bono, Hidemasa, ...
Although many studies on alternative splicing of specific genes have been reported in the literature, the general mechanism that regulates alternative splicing has not been clearly understood. In...
Identification of Putative Noncoding RNAs Among the RIKEN Mouse Full-Length cDNA Collection
Numata, Koji, Kanai, Akio, Saito, Rintaro, Kondo, Shinji, Adachi, Jun, Wilming, Laurens G., ...
With the sequencing and annotation of genomes and transcriptomes of several eukaryotes, the importance of noncoding RNA (ncRNA)—RNA molecules that are not translated to protein products—has...
Comparative Analysis of Physical Maps of Four Bacillus subtilis (natto) Genomes
Qiu, Dongru, Fujita, Kyoko, Sakuma, Yuko, Tanaka, Teruo, Ohashi, Yoshiaki, Ohshima, Hideyuki, ...
The complete SfiI and I-CeuI physical maps of four Bacillus subtilis (natto) strains, which were previously isolated as natto (fermented soybean) starters, were constructed to elucidate the genome...
Cleavage of double-stranded RNA by RNase HI from a thermoacidophilic archaeon, Sulfolobus tokodaii 7
Ohtani, Naoto, Yanagawa, Hiroshi, Tomita, Masaru, Itaya, Mitsuhiro
ST0753, the orthologous gene of Type 1 RNase H found in a thermoacidophilic archaeon, Sulfolobus tokodaii, was analyzed. The recombinant ST0753 protein exhibited RNase H activity in both in vivo and...
Ohtani, Naoto, Yanagawa, Hiroshi, Tomita, Masaru, Itaya, Mitsuhiro
All the archaeal genomes sequenced to date contain a single Type 2 RNase H gene. We found that the genome of a halophilic archaeon, Halobacterium sp. NRC-1, contains an open reading frame with...
Hybrid dynamic/static method for large-scale simulation of metabolism
Yugi, Katsuyuki, Nakayama, Yoichi, Kinoshita, Ayako, Tomita, Masaru
A microarray data-based semi-kinetic method for predicting quantitative dynamics of genetic networks
Yugi, Katsuyuki, Nakayama, Yoichi, Kojima, Shigen, Kitayama, Tomoya, Tomita, Masaru
ITOH, HITOMI, WASHIO, TAKANORI, TOMITA, MASARU
We previously reported a computational approach to infer alternative splicing patterns from Mus musculus full-length cDNA clones and microarray data. Although we predicted a large number of...
Archaeal Pyrococcus furiosus thymidylate synthase 1 is an RNA-binding protein
Kanai, Akio, Sato, Asako, Imoto, Jun, Tomita, Masaru
Using a stem–loop RNA oligonucleotide (19-mer) containing an AUG sequence in the loop region as a probe, we screened the protein library from a hyperthermophilic archaeon, Pyrococcus furiosus, and...
GEM System: automatic prototyping of cell-wide metabolic pathway models from genomes
Arakawa, Kazuharu, Yamada, Yohei, Shinoda, Kosaku, Nakayama, Yoichi, Tomita, Masaru
Large-scale identification of protein–protein interaction of Escherichia coli K-12
Arifuzzaman, Mohammad, Maeda, Maki, Itoh, Aya, Nishikata, Kensaku, Takita, Chiharu, Saito, Rintaro, ...
Protein–protein interactions play key roles in protein function and the structural organization of a cell. A thorough description of these interactions should facilitate elucidation of cellular...
Characteristics and clustering of human ribosomal protein genes
Ishii, Kyota, Washio, Takanori, Uechi, Tamayo, Yoshihama, Maki, Kenmochi, Naoya, Tomita, Masaru
Parameter estimation for stiff equations of biosystems using radial basis function networks
Matsubara, Yoshiya, Kikuchi, Shinichi, Sugimoto, Masahiro, Tomita, Masaru
HybGFS: a hybrid method for genome-fingerprint scanning
Shinoda, Kosaku, Yachie, Nozomu, Masuda, Takeshi, Sugiyama, Naoyuki, Sugimoto, Masahiro, Soga, Tomoyoshi, ...
MathDAMP: a package for differential analysis of metabolite profiles
Baran, Richard, Kochi, Hayataro, Saito, Natsumi, Suematsu, Makoto, Soga, Tomoyoshi, Nishioka, Takaaki, ...
Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection
Baba, Tomoya, Ara, Takeshi, Hasegawa, Miki, Takai, Yuki, Okumura, Yoshiko, Baba, Miki, ...
We have systematically made a set of precisely defined, single-gene deletions of all nonessential genes in Escherichia coli K-12. Open-reading frame coding regions were replaced with a kanamycin...
Visualization of three-way comparisons of omics data
Baran, Richard, Robert, Martin, Suematsu, Makoto, Soga, Tomoyoshi, Tomita, Masaru
Ogawa, Tadashi, Murakami, Keiko, Mori, Hirotada, Ishii, Nobuyoshi, Tomita, Masaru, Yoshin, Masataka
Phosphoenolpyruvate inhibited Escherichia coli NADP-isocitrate dehydrogenase allosterically (Ki of 0.31 mM) and isocitrate lyase uncompetitively (Ki′ of 0.893 mM). Phosphoenolpyruvate enhances the...
Modeling Hsp70-Mediated Protein Folding
Hu, Bin, Mayer, Matthias P., Tomita, Masaru
The Hsp70 chaperone system is the major molecular chaperone system that assists protein-folding processes in all cells. To understand these processes, we analyzed the kinetic characteristics of the...
Sequential Logic Model Deciphers Dynamic Transcriptional Control of Gene Expressions
Yeo, Zhen Xuan, Wong, Sum Thai, Arjunan, Satya Nanda Vel, Piras, Vincent, Tomita, Masaru, Selvarajoo, Kumar, ...
Sugahara, Junichi, Yachie, Nozomu, Arakawa, Kazuharu, Tomita, Masaru
In archaeal species, several transfer RNA genes have been reported to contain endogenous introns. Although most of the introns are located at anticodon loop regions between nucleotide positions 37...
Fujishima, Kosuke, Sugahara, Junichi, Tomita, Masaru, Kanai, Akio
The discovery of separate 5′ and 3′ halves of transfer RNA (tRNA) molecules—so-called split tRNA—in the archaeal parasite Nanoarchaeum equitans made us wonder whether ancestral tRNA was...
Variation in the Correlation of G + C Composition with Synonymous Codon Usage Bias among Bacteria
Suzuki, Haruo, Saito, Rintaro, Tomita, Masaru
G + C composition at the third codon position (GC3) is widely reported to be correlated with synonymous codon usage bias. However, no quantitative attempt has been made to compare the extent of this...
Implications from a Network-Based Topological Analysis of Ubiquitin Unfolding Simulations
Krishnan, Arun, Giuliani, Alessandro, Zbilut, Joseph P., Tomita, Masaru
Large-scale phosphorylation mapping reveals the extent of tyrosine phosphorylation in Arabidopsis
Sugiyama, Naoyuki, Nakagami, Hirofumi, Mochida, Keiichi, Daudi, Arsalan, Tomita, Masaru, Shirasu, Ken, ...
Protein phosphorylation regulates a wide range of cellular processes. Here, we report the proteome-wide mapping of in vivo phosphorylation sites in Arabidopsis by using complementary phosphopeptide...
Time-resolved metabolomics reveals metabolic modulation in rice foliage
Sato, Shigeru, Arita, Masanori, Soga, Tomoyoshi, Nishioka, Takaaki, Tomita, Masaru
Yoshida, Satoshi, Imoto, Jun, Minato, Toshiko, Oouchi, Rie, Sugihara, Mao, Imai, Takeo, ...
Sulfite plays an important role in beer flavor stability. Although breeding of bottom-fermenting Saccharomyces strains that produce high levels of SO2 is desirable, it is complicated by the fact that...
Simulation of developmental changes in action potentials with ventricular cell models
Itoh, Hitomi, Naito, Yasuhiro, Tomita, Masaru
During cardiomyocyte development, early embryonic ventricular cells show spontaneous activity that disappears at a later stage. Dramatic changes in action potential are mediated by developmental...
Hsp70 chaperones assist protein folding by cycling between the ATP-bound T state with low affinity for substrates and the ADP-bound R state with high affinity for substrates. The transition from the...
Signaling Flux Redistribution at Toll-Like Receptor Pathway Junctions
Selvarajoo, Kumar, Takada, Yasunari, Gohda, Jin, Helmy, Mohamed, Akira, Shizuo, Tomita, Masaru, ...
Various receptors on cell surface recognize specific extracellular molecules and trigger signal transduction altering gene expression in the nucleus. Gain or loss-of-function mutations of one...
Genome Projector: zoomable genome map with multiple views
Arakawa, Kazuharu, Tamaki, Satoshi, Kono, Nobuaki, Kido, Nobuhiro, Ikegami, Keita, Ogawa, Ryu, ...
Predicting Novel Features of Toll-Like Receptor 3 Signaling in Macrophages
Helmy, Mohamed, Gohda, Jin, Inoue, Jun-ichiro, Tomita, Masaru, Tsuchiya, Masa, Selvarajoo, Kumar
The Toll-like receptor (TLR) 3 plays a critical role in mammalian innate immune response against viral attacks by recognizing double-stranded RNA (dsRNA) or its synthetic analog...
Riou Matsushima, Akiko Kawase, Hisako Nakano, Kanako Saito, Masaru Tomita
In this work, we try to model and simulate human red blood cell using E-CELL system, a generic software for simulation of cellular processes [1]. Human red blood cell has been well-studied in last...
On Low Frequency of CpG Dinucleotides in Bacterial Genomes Mami Goto
Takanori Washio, Masaru Tomita
CpG depletion is a phenomenon known to be caused by CpG DNA methylation. Although CpG DNA methylation is believed to be a feature of vertebrates and plants [1], we have found that some procaryote...
Modeling Human, Red Blood Cell, Riou Matsushima, Akiko Kawase, Hisako Nakano, Kanako Saito, ...
In this work, we try to model and simulate human red blood cell using E-CELL system, a generic software for simulation of cellular processes [1]. Human red blood cell has been well-studied in last...
Tsuchiya, Masa, Piras, Vincent, Choi, Sangdun, Akira, Shizuo, Tomita, Masaru, Giuliani, Alessandro, ...
Large-scale gene expression studies have mainly focused on highly expressed and ‘discriminatory’ genes to decipher key regulatory processes. Biological responses are consequence of the concerted...
Stabilizing synthetic data in the DNA of living organisms
Yachie, Nozomu, Ohashi, Yoshiaki, Tomita, Masaru
Data-encoding synthetic DNA, inserted into the genome of a living organism, is thought to be more robust than the current media. Because the living genome is duplicated and copied into new...
Arakawa, Kazuharu, Tomita, Masaru
Bacterial chromosomes are partly shaped by the functional requirements for efficient replication, which lead to strand bias as commonly characterized by the excess of guanines over cytosines in the...
Arakawa, Kazuharu, Tomita, Masaru
Circular bacterial chromosomes have highly polarized nucleotide composition in the two replichores, and this genomic strand asymmetry can be visualized using GC skew graphs. Here we propose and...
Network Features and Pathway Analyses of a Signal Transduction Cascade
Yanashima, Ryoji, Kitagawa, Noriyuki, Matsubara, Yoshiya, Weatheritt, Robert, Oka, Kotaro, Kikuchi, Shinichi, ...
The scale-free and small-world network models reflect the functional units of networks. However, when we investigated the network properties of a signaling pathway using these models, no significant...
Kosugi, Shunichi, Hasebe, Masako, Tomita, Masaru, Yanagawa, Hiroshi
The cell cycle-dependent nucleocytoplasmic transport of proteins is predominantly regulated by CDK kinase activities; however, it is currently difficult to predict the proteins thus regulated,...
Fujishima, Kosuke, Sugahara, Junichi, Kikuta, Kaoru, Hirano, Reiko, Sato, Asako, Tomita, Masaru, ...
Transfer RNA (tRNA) is essential for decoding the genome sequence into proteins. In Archaea, previous studies have revealed unique multiple intron-containing tRNAs and tRNAs that are encoded on 2...
Kanai, Akio, Sato, Asako, Fukuda, Yoko, Okada, Kiyoshi, Matsuda, Takashi, Sakamoto, Taiichi, ...
Using an expression protein library of a hyperthermophilic archaeon, Pyrococcus furiosus, we identified a gene (PF0027) that encodes a protein with heat-stable cyclic nucleotide phosphodiesterase...
A web server for interactive and zoomable Chaos Game Representation images
Arakawa, Kazuharu, Oshita, Kazuki, Tomita, Masaru
Chaos Game Representation (CGR) is a generalized scale-independent Markov transition table, which is useful for the visualization and comparative study of genomic signature, or for the study of...
Nakahigashi, Kenji, Toya, Yoshihiro, Ishii, Nobuyoshi, Soga, Tomoyoshi, Hasegawa, Miki, Watanabe, Hisami, ...
Central carbon metabolism is a basic and exhaustively analyzed pathway. However, the intrinsic robustness of the pathway might still conceal uncharacterized reactions. To test this hypothesis, we...
Pathway Projector: Web-Based Zoomable Pathway Browser Using KEGG Atlas and Google Maps API
Kono, Nobuaki, Arakawa, Kazuharu, Ogawa, Ryu, Kido, Nobuhiro, Oshita, Kazuki, Ikegami, Keita, ...
Fujishima, Kosuke, Komasa, Mizuki, Kitamura, Sayaka, Suzuki, Haruo, Tomita, Masaru, Kanai, Akio
Proteins play a critical role in complex biological systems, yet about half of the proteins in publicly available databases are annotated as functionally unknown. Proteome-wide functional...